You get better MPG if you limit your top end air flow. By definition, you won't be able to generate as much HP. Throttle limiting or air baffles can increase your apparent MPG (depending on how you drive) at the expense of power.

The "kicking" at idle is usually more pronounced on 3.0's then 4.0's. However, there are many reports of aftermarket air intakes creating problems on 4.0's when the air flow changes. Perhaps this is like that.

I would clean your MAF using electronic cleaner or carb cleaner. Do NOT use an electronic cleaner with lubricating properties! It's possible when you were doing the work that something got in there.